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Genome-wide association mapping of root traits in a japonica rice panel.

Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A, Ahmadi N, Dingkuhn M - PLoS ONE (2013)

Bottom Line: Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04.The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion.Several likely candidate genes were found in close proximity to these loci.

View Article: PubMed Central - PubMed

Affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France.

ABSTRACT
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

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Related in: MedlinePlus

General view of the Rhizoscope phenotyping system.
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pone-0078037-g002: General view of the Rhizoscope phenotyping system.

Mentions: The plants were grown in a hydroponic system set in a growth chamber developed by Cirad and called Rhizoscope that has the capacity to handle 192 plants at a time [41]. The experimental unit was a sandwich of two 50 cm × 20 cm × 2 cm Plexiglas plates (internal dimensions) filled with glass beads of 1.5 mm diameter, called a rhizobox (Figure 1). A trap at the bottom of the sandwich enabled the easy removal of the beads at the end of the experiment. This device greatly simplifies the cleaning step while imposing some degree of mechanical resistance to root penetration that is closer to normal soil conditions than is a pure hydroponics system. The rhizobox can be completely opened as well. Similar to nailboard systems, each rhizobox contains a grid of nails, which holds the root system in place after bead removal when the sandwich is opened. The 192 rhizoboxes were set in four large tanks with a capacity of 48 rhizoboxes each (Figure 2). An aerated nutrient solution (volume of 3,000 l) was circulated continuously through the rhizoboxes (composition in Table S2). After pre-germinating several seeds per accession at 28°C for three days, one well developed seedling per rhizobox was set on the top of the beads. The solution pH was adjusted to and maintained at 5.4±0.2 by automatic pH controllers. A cooling system maintained the temperature of the solution at 27±1°C. The conditions in the growth chamber were 28°C during the day and 25°C at night with a 12:12 photoperiod. The radiation was 400 to 450 µmol photons per m2 per s (PAR). The relative humidity was set to 55%.


Genome-wide association mapping of root traits in a japonica rice panel.

Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A, Ahmadi N, Dingkuhn M - PLoS ONE (2013)

General view of the Rhizoscope phenotyping system.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3818351&req=5

pone-0078037-g002: General view of the Rhizoscope phenotyping system.
Mentions: The plants were grown in a hydroponic system set in a growth chamber developed by Cirad and called Rhizoscope that has the capacity to handle 192 plants at a time [41]. The experimental unit was a sandwich of two 50 cm × 20 cm × 2 cm Plexiglas plates (internal dimensions) filled with glass beads of 1.5 mm diameter, called a rhizobox (Figure 1). A trap at the bottom of the sandwich enabled the easy removal of the beads at the end of the experiment. This device greatly simplifies the cleaning step while imposing some degree of mechanical resistance to root penetration that is closer to normal soil conditions than is a pure hydroponics system. The rhizobox can be completely opened as well. Similar to nailboard systems, each rhizobox contains a grid of nails, which holds the root system in place after bead removal when the sandwich is opened. The 192 rhizoboxes were set in four large tanks with a capacity of 48 rhizoboxes each (Figure 2). An aerated nutrient solution (volume of 3,000 l) was circulated continuously through the rhizoboxes (composition in Table S2). After pre-germinating several seeds per accession at 28°C for three days, one well developed seedling per rhizobox was set on the top of the beads. The solution pH was adjusted to and maintained at 5.4±0.2 by automatic pH controllers. A cooling system maintained the temperature of the solution at 27±1°C. The conditions in the growth chamber were 28°C during the day and 25°C at night with a 12:12 photoperiod. The radiation was 400 to 450 µmol photons per m2 per s (PAR). The relative humidity was set to 55%.

Bottom Line: Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04.The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion.Several likely candidate genes were found in close proximity to these loci.

View Article: PubMed Central - PubMed

Affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France.

ABSTRACT
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

Show MeSH
Related in: MedlinePlus